Ubuntu :: USB Serial Adapter Unreliable On Startup

I am using a Sealink PN 2202 USB serial adapter on a linux box (Ubuntu 10.4) running kernel 2.6.32-28-generic. I have written a perl script to simply log the incoming RS232 data (9600 8N2) and it works fine when I start it from a bash shell:
perl /home/pk/PerlCode/RS232_D4_v11.pl

However, I need the computer to boot and start logging after a POR. If I try to use Startup Manager to execute my script everything seems ok but I randomly loose about 20% of the incoming RS232 data. In Startup Manager I use the command
gnome-terminal --title="D4 RS232 Log" --execute bash -c "perl
/home/pk/PerlCode/RS232_D4_v11.pl"

If I close the automatically-started script and restart it from a bash shell, I again will randomly loose about 20% of the incoming RS232 data. It almost seems like I have screwed up the driver by using the Startup Manager. The only way I can get reliable logging again is to remove the script from Startup Manager, then restart the computer and manually launch the perl script. I was thinking that maybe the order in which the driver was loaded and perl script started might be an issue. So I tried a bash script that sleeps for 15seconds, then starts the perl script. Again, I loose random pieces of incoming data when this is initiated by Startup Manager.

Here is some more info:
lsusb
Bus 005 Device 001: ID 1d6b:0001 Linux Foundation 1.1 root hub
Bus 004 Device 001: ID 1d6b:0001 Linux Foundation 1.1 root hub
Bus 003 Device 001: ID 1d6b:0001 Linux Foundation 1.1 root hub
Bus 002 Device 004: ID 0c52:2223 Sealevel Systems, Inc.
Bus 002 Device 003: ID 0c52:2213 Sealevel Systems, Inc.
Bus 002 Device 002: ID 03eb:3301 Atmel Corp. at43301 4-Port Hub
Bus 002 Device 001: ID 1d6b:0001 Linux Foundation 1.1 root hub
Bus 001 Device 001: ID 1d6b:0002 Linux Foundation 2.0 root hub .....

sudo cat /proc/tty/driver/usbserial
usbserinfo:1.0 driver:2.0
0: module:ftdi_sio name:"FTDI USB Serial Device" vendor:0c52
product:2213 num_ports:1 port:1 path:usb-0000:00:1d.0-2.1
1: module:ftdi_sio name:"FTDI USB Serial Device" vendor:0c52
product:2223 num_ports:1 port:1 path:usb-0000:00:1d.0-2.2

ls -al /dev/ttyUSB*
crw-rw---- 1 root dialout 188, 0 2011-03-08 09:56 /dev/ttyUSB0
crw-rw---- 1 root dialout 188, 1 2011-03-08 09:56 /dev/ttyUSB1
I am a member of the group dialout.

I though it may have something to do with su vs my ownership of files. If I do a sudo chmod 777 /dev/ttyUSB* then
ls -al /dev/ttyUSB*
crwxrwxrwx 1 root dialout 188, 0 2011-03-08 09:56 /dev/ttyUSB0
crwxrwxrwx 1 root dialout 188, 1 2011-03-08 09:56 /dev/ttyUSB1

However, after rebooting it reverts to
ls -al /dev/ttyUSB*
crw-rw---- 1 root dialout 188, 0 2011-03-08 09:56 /dev/ttyUSB0
crw-rw---- 1 root dialout 188, 1 2011-03-08 09:56 /dev/ttyUSB1